RetrogeneDB ID: | retro_ocun_1794 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018899:83964..85491(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TCF7L1 | ||
| Ensembl ID: | ENSOCUG00000008749 | ||
| Aliases: | None | ||
| Description: | transcription factor 7-like 1 (T-cell specific, HMG-box) [Source:HGNC Symbol;Acc:11640] |
Retrocopy-Parental alignment summary:
>retro_ocun_1794
CAGAGCTGCAGCTCGGACTCAGAGGCGGAGAGGCACCCGCAGCCCTCCCGGGACACTTTCCAGAAGCCGCGGGACTATTT
CACCGAAGTGAGAAGGCCCCAGGACGGCGCGTTCTTCAAGGGCCCCCTTACCCTGGGTACCCCTTCCTGATGATCCCGGA
CCTGAGCAACCCCTACCTCTCCAACGGACCCCTGTCTCCGGGAGGAGCATGCATGTACCTGCAGATGAAATGGCCCCTCC
TCGACGTCCCCTCCAGTGCCACAGTCAAGGACACGAGGTCACCGTCTCCGGCACACTTGTCCAATAAAGTTCCTGTTTGT
GCAGCACCCACATCACATGCACCCGTTGACACCGCTCATCACCTAACGCAATGACCACTTCTCCGCCGGCTCCCCTCCAA
CACACCTCTCCCCGGAGATCAATCCAAAGACAGGAATTCCCCGGCCCCCTCATCCATCTGAGCTGTCACTGTATCACCCA
CTGTCCCCAGGAGCTGTCAGACAAATCCCCCACCCCCTTGGCTGGCTCATCCCACAGCAATGACAGCCCATGTACTCCCT
TCCGCCTGGTGGCTTCGGCACCCTTACCCTGCCCTCGCCATGAACCCCTCAATGTCCAGCCTGGTTTCCAGCTGCTTCTC
CCTTCACAGGGTGGCCCCCGCCCATCCTTGCCTGCCCACCTCAGGGATCCTGCACCCCACCATTGTCAAGCAGGAGCCAG
CACCTCCCAGCCTGAGCCCCACGGTGAGCGCGAAGTCACCCGTGACCATGAAGAAGGAGGAGAAGAAACCCCACATGAAG
AAGCCCCTGAATGCCTTCATGTTGTATATGAAGAAGATGAGGGCCAAGGTGGTGGCTGAGTGCACCCTGAAGGAGAGTGC
TGCCATCAACCAGATGCTGGGGAGGAAGTGGCACAACCTGTCGCAGGAAGAACAGGTCAGGCACTAGAAGCTGGCCCAGA
AGGAGCGGCAGCTTCACTCCCAGCTCTACCCGACCAGCTCGGTAGGGACAACTACAGTAAGAAAAAGAAGAGGAAGTGAG
AGAAGCCGCTGTTGCAGACGCAGACGCAGTCACAGCAGCACGTCCAAGAGGCAGAGGGTGCCCTGGCCTCCAAGAGCAAG
AAGCCACGTGTCCAGTACCTGCCCCCCGAGAGGCCTTGTGACAGCCCTGCCTCCTCCCACGGCAGCATGTTGGACTCCCC
TGCCACCCCCTCCACGGCCTTGGACTCACCAGCTGACCCTGCTGCCACCCACTCCAAGCAAGACCAGCCCCTCTCCCACA
CCACCAAGCCAGAGACCTGGGCCCAGCTGGCTCTGCACTCGGCTGCTGTCCTGGCAGCCAAGGCTGCAGCCACGTCCTCC
GGCCAGATGGGCAGCCAGCCTCCCCTCCTGTCCCGGCCCTCCCGCTGGGGTCCGTGCCCACCACTCTGCTGACTTCTCCC
CCCTCTTTCCCAGCCATGCTGCACACCCACCAGACCCTCCCTGTGCTCCAGGCCCAGCCTCTTTCCTTGGTCACCAAGTC
TGCCCAC
ORF - retro_ocun_1794 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.15 % |
| Parental protein coverage: | 99.04 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | RAAALNSEAERRPQPSRDAFQKPRDYFAEVRRPQDGAFFKGP-PYPGYPFLMIPDLSSPYLSNGPLSPGG |
| ......SEAER.PQPSRD.FQKPRDYF.EVRRPQDGAFFKGP.PYPGYPFLMIPDLS.PYLSNGPLSPGG | |
| Retrocopy | QSCSSDSEAERHPQPSRDTFQKPRDYFTEVRRPQDGAFFKGP<PYPGYPFLMIPDLSNPYLSNGPLSPGG |
| Parental | ARTYLQMKWPLLDVPSSATVKDARSPSPAHLSNKVPV-VQHPHHMHPLTPLITYSNDHFSPGSPPTHLSP |
| A..YLQMKWPLLDVPSSATVKD.RSPSPAHLSNKVPV.VQHPHHMHPLTPLIT..NDHFS.GSPPTHLSP | |
| Retrocopy | ACMYLQMKWPLLDVPSSATVKDTRSPSPAHLSNKVPV>VQHPHHMHPLTPLIT*RNDHFSAGSPPTHLSP |
| Parental | EIDPKTGIPRPPHPSELSPYYPLSPGAVGQIPHPLGWLVPQQGQPMYSLPPGGF-RHPYPALAMNASMSS |
| EI.PKTGIPRPPHPSELS.Y.PLSPGAV.QIPHPLGWL.PQQ.QPMYSLPPGGF.RHPYPALAMN.SMSS | |
| Retrocopy | EINPKTGIPRPPHPSELSLYHPLSPGAVRQIPHPLGWLIPQQ*QPMYSLPPGGF<RHPYPALAMNPSMSS |
| Parental | LVSSRFSPHMVAPAHPGLPTSGIPHPAIVSPIVKQEPAPPSLSPAVSAKSPVTVKKEEEKKPHVKKPLNA |
| LVSS.FS.H.VAPAHP.LPTSGI.HP.....IVKQEPAPPSLSP.VSAKSPVT.KKEE.KKPH.KKPLNA | |
| Retrocopy | LVSSCFSLHRVAPAHPCLPTSGILHPT----IVKQEPAPPSLSPTVSAKSPVTMKKEE-KKPHMKKPLNA |
| Parental | FMLYMKEMRAKVVAECTLKESAAINQILGRKWHNLSREEQAKYYELARKERQLHSQLYPTWSA-RDNYGK |
| FMLYMK.MRAKVVAECTLKESAAINQ.LGRKWHNLS.EEQ.....LA.KERQLHSQLYPT.S..RDNY.K | |
| Retrocopy | FMLYMKKMRAKVVAECTLKESAAINQMLGRKWHNLSQEEQVRH*KLAQKERQLHSQLYPTSSV<RDNYSK |
| Parental | KKKRKREKQLSQTQTQSQQHVQEAEGALASKSKKPCVQYLPPEKPCDSPASSHGSMLDSPATPSAALASP |
| KKKRK.EK.L.QTQTQSQQHVQEAEGALASKSKKP.VQYLPPE.PCDSPASSHGSMLDSPATPS.AL.SP | |
| Retrocopy | KKKRK*EKPLLQTQTQSQQHVQEAEGALASKSKKPRVQYLPPERPCDSPASSHGSMLDSPATPSTALDSP |
| Parental | AAPAATHSEQAQPLSLTTKPETRAQLALHSAAFLSAKAAATSPGQMGSQPPLLSRP-LPLGSVPTALLTS |
| A.PAATHS.Q.QPLS.TTKPET.AQLALHSAA.L.AKAAATS.GQMGSQPPLLSRP.LPLGSVPT.LLTS | |
| Retrocopy | ADPAATHSKQDQPLSHTTKPETWAQLALHSAAVLAAKAAATSSGQMGSQPPLLSRP<LPLGSVPTTLLTS |
| Parental | PPSFPATLHAHQTLPVLQAQPLSLVTKSAH |
| PPSFPA.LH.HQTLPVLQAQPLSLVTKSAH | |
| Retrocopy | PPSFPAMLHTHQTLPVLQAQPLSLVTKSAH |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP017611_brain | 0 .33 RPM | 9 .77 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .86 RPM |
| SRP017611_liver | 0 .15 RPM | 4 .24 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1794 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1794 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1794 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000008749 | 1 retrocopy |
retro_ocun_1794 ,
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